I've been working on integrating the crew here with the SFS system, so that they get saved with the ship they are in, and then respawn later. Easier said than done though... to maintain consistency with the SFS system, the crew needs a complete SFS representation, so I'm having to write a whole lot more code than I initially expected. But that's ok, because if experience is any reference, this should be a very robust and flexible solution (because it follow the same logic as the ships and parts in the SFS system).

The way I'm doing this is something like this: The vessels themselves will hold no crew. Their parts will. That is, a vessel definition will only provide convenience functions to manage crew, but what actually holds the crew references are the parts. That is because vessels are too generic to actually hold crew. If you carry a passenger cabin module into a suborbital joyride (which might be a possibility in the future) and then detach the module and fire yourself into a closed orbit, your passengers will now be on a very different trip than yours, and quite obviously in another spacecraft as well. So it's the parts that need to hold the crew in them.

Ok, not too bad, but then we hit another problem. The crew will only actually exist on the active vessel. On the others, they are de-spawned, and exist only as abstract objects. The problem is, if we then generate a scene backup (as with autosaving), what do we use to build the crew backup? The parts exist, so they will be backed up fine, but the crew might not.

Fortunately though, this isn't the first time we've faced this issue. The vessels themselves are doing something very similar with their in-flight unloading scheme. If a vessel is unloaded, it will return the reference to it's last generated backup. Trouble is, if a vessel is unloaded, it's own instance isn't quite dead... only it's parts are. So that means a vessel can hold it's own backup even if it's unloaded, as opposed to the crew, which will be completely removed from the game at that point.
To solve this issue then, I think we might get away with storing the crew backups in the parts that contain them... It's a small inconsistency with the way vessels do things, but it should work just as well I think.